From de7e84654ad81992793ed253c2744c67aaa532db Mon Sep 17 00:00:00 2001 From: Pau Andrio Date: Thu, 4 Jul 2024 10:47:48 +0200 Subject: [PATCH] [UPDATE] Adding sandbox_path property to the json schemas --- biobb_cmip/docs/source/command_line.md | 5 +++++ biobb_cmip/json_schemas/cmip_ignore_residues.json | 6 ++++++ biobb_cmip/json_schemas/cmip_prepare_pdb.json | 6 ++++++ biobb_cmip/json_schemas/cmip_prepare_structure.json | 6 ++++++ biobb_cmip/json_schemas/cmip_run.json | 6 ++++++ biobb_cmip/json_schemas/cmip_titration.json | 6 ++++++ 6 files changed, 35 insertions(+) diff --git a/biobb_cmip/docs/source/command_line.md b/biobb_cmip/docs/source/command_line.md index b766278..bd673d1 100644 --- a/biobb_cmip/docs/source/command_line.md +++ b/biobb_cmip/docs/source/command_line.md @@ -44,6 +44,7 @@ Config parameters for this building block: * **fix_backbone_atoms** (*boolean*): (True) Add missing O, OXT backbone atoms.. * **remove_tmp** (*boolean*): (True) Remove temporal files.. * **restart** (*boolean*): (False) Do not execute if output files exist.. +* **sandbox_path** (*string*): (./) Parent path to the sandbox directory.. ### YAML #### [Common config file](https://github.com/bioexcel/biobb_cmip/blob/master/biobb_cmip/test/data/config/config_cmip_prepare_pdb.yml) ```python @@ -104,6 +105,7 @@ Config parameters for this building block: * **ignore_all** (*boolean*): (False) Mark all the residues in the PDB file.. * **remove_tmp** (*boolean*): (True) Remove temporal files.. * **restart** (*boolean*): (False) Do not execute if output files exist.. +* **sandbox_path** (*string*): (./) Parent path to the sandbox directory.. ### YAML #### [Common config file](https://github.com/bioexcel/biobb_cmip/blob/master/biobb_cmip/test/data/config/config_cmip_ignore_residues.yml) ```python @@ -173,6 +175,7 @@ Config parameters for this building block: * **binary_path** (*string*): (titration) Path to the CMIP Titration executable binary.. * **remove_tmp** (*boolean*): (True) Remove temporal files.. * **restart** (*boolean*): (False) Do not execute if output files exist.. +* **sandbox_path** (*string*): (./) Parent path to the sandbox directory.. * **container_path** (*string*): (None) Path to the binary executable of your container.. * **container_image** (*string*): (cmip/cmip:latest) Container Image identifier.. * **container_volume_path** (*string*): (/data) Path to an internal directory in the container.. @@ -305,6 +308,7 @@ Config parameters for this building block: * **binary_path** (*string*): (cmip) Path to the CMIP cmip executable binary.. * **remove_tmp** (*boolean*): (True) Remove temporal files.. * **restart** (*boolean*): (False) Do not execute if output files exist.. +* **sandbox_path** (*string*): (./) Parent path to the sandbox directory.. * **container_path** (*string*): (None) Path to the binary executable of your container.. * **container_image** (*string*): (cmip/cmip:latest) Container Image identifier.. * **container_volume_path** (*string*): (/data) Path to an internal directory in the container.. @@ -413,6 +417,7 @@ Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: * **remove_tmp** (*boolean*): (True) Remove temporal files.. * **restart** (*boolean*): (False) Do not execute if output files exist.. +* **sandbox_path** (*string*): (./) Parent path to the sandbox directory.. * **container_path** (*string*): (None) Path to the binary executable of your container.. * **container_image** (*string*): (cmip/cmip:latest) Container Image identifier.. * **container_volume_path** (*string*): (/data) Path to an internal directory in the container.. diff --git a/biobb_cmip/json_schemas/cmip_ignore_residues.json b/biobb_cmip/json_schemas/cmip_ignore_residues.json index e4333a1..c55c5dd 100644 --- a/biobb_cmip/json_schemas/cmip_ignore_residues.json +++ b/biobb_cmip/json_schemas/cmip_ignore_residues.json @@ -79,6 +79,12 @@ "default": false, "wf_prop": true, "description": "Do not execute if output files exist." + }, + "sandbox_path": { + "type": "string", + "default": "./", + "wf_prop": true, + "description": "Parent path to the sandbox directory." } } } diff --git a/biobb_cmip/json_schemas/cmip_prepare_pdb.json b/biobb_cmip/json_schemas/cmip_prepare_pdb.json index 835ca79..d1e2a95 100644 --- a/biobb_cmip/json_schemas/cmip_prepare_pdb.json +++ b/biobb_cmip/json_schemas/cmip_prepare_pdb.json @@ -97,6 +97,12 @@ "default": false, "wf_prop": true, "description": "Do not execute if output files exist." + }, + "sandbox_path": { + "type": "string", + "default": "./", + "wf_prop": true, + "description": "Parent path to the sandbox directory." } } } diff --git a/biobb_cmip/json_schemas/cmip_prepare_structure.json b/biobb_cmip/json_schemas/cmip_prepare_structure.json index 8b49dfe..2a61f52 100644 --- a/biobb_cmip/json_schemas/cmip_prepare_structure.json +++ b/biobb_cmip/json_schemas/cmip_prepare_structure.json @@ -102,6 +102,12 @@ "wf_prop": true, "description": "Do not execute if output files exist." }, + "sandbox_path": { + "type": "string", + "default": "./", + "wf_prop": true, + "description": "Parent path to the sandbox directory." + }, "container_path": { "type": "string", "default": null, diff --git a/biobb_cmip/json_schemas/cmip_run.json b/biobb_cmip/json_schemas/cmip_run.json index 67d7f4f..6f04ca4 100644 --- a/biobb_cmip/json_schemas/cmip_run.json +++ b/biobb_cmip/json_schemas/cmip_run.json @@ -343,6 +343,12 @@ "wf_prop": true, "description": "Do not execute if output files exist." }, + "sandbox_path": { + "type": "string", + "default": "./", + "wf_prop": true, + "description": "Parent path to the sandbox directory." + }, "container_path": { "type": "string", "default": null, diff --git a/biobb_cmip/json_schemas/cmip_titration.json b/biobb_cmip/json_schemas/cmip_titration.json index f4e4673..6580625 100644 --- a/biobb_cmip/json_schemas/cmip_titration.json +++ b/biobb_cmip/json_schemas/cmip_titration.json @@ -142,6 +142,12 @@ "wf_prop": true, "description": "Do not execute if output files exist." }, + "sandbox_path": { + "type": "string", + "default": "./", + "wf_prop": true, + "description": "Parent path to the sandbox directory." + }, "container_path": { "type": "string", "default": null,